6QX9

Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Mechanism of 5' splice site transfer for human spliceosome activation.

Charenton, C.Wilkinson, M.E.Nagai, K.

(2019) Science 364: 362-367

  • DOI: 10.1126/science.aax3289
  • Primary Citation of Related Structures:  
    6QW6, 6QX9

  • PubMed Abstract: 
  • The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome ...

    The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. ccharent@mrc-lmb.cam.ac.uk mwilkin@mrc-lmb.cam.ac.uk kn@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinC [auth 5O]357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40PRP8BPSFP38WDR57
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 4D [auth B4]424Homo sapiensMutation(s): 0 
Gene Names: SF3B4SAP49
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3E [auth 13], RA [auth 23], UA [auth 43], V [auth 53]126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp4F [auth 4B]522Homo sapiensMutation(s): 0 
Gene Names: PRPF4PRP4
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EVA [auth 1e], EB [auth 2e], N [auth 4e], G [auth 5e]92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein 70 kDaI [auth 1K]437Homo sapiensMutation(s): 0 
Gene Names: SNRNP70RNPU1ZRPU1SNRP70U1AP1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp31J [auth 4C]499Homo sapiensMutation(s): 0 
Gene Names: PRPF31PRP31
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1BA [auth 11], LB [auth 21], K [auth 41], JA [auth 51]119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein 42L [auth R]480Homo sapiensMutation(s): 0 
Gene Names: RBM42
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FM [auth 1f], Y [auth 2f], OA [auth 4f], HA [auth 5f]86Homo sapiensMutation(s): 0 
Gene Names: SNRPFPBSCF
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm6O [auth 66]80Homo sapiensMutation(s): 0 
Gene Names: LSM6
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa proteinP [auth X]155Homo sapiensMutation(s): 0 
Gene Names: SNRNP27
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2CB [auth 12], Q [auth 22], CA [auth 42], BB [auth 52]118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2SNRPD1
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm7S [auth 67]103Homo sapiensMutation(s): 0 
Gene Names: LSM7
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm2T [auth 62]95Homo sapiensMutation(s): 0 
Gene Names: LSM2C6orf28G7B
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''U [auth 2B]225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 2W [auth A2]209Homo sapiensMutation(s): 0 
Gene Names: SF3A2SAP62
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 2X [auth B2]895Homo sapiensMutation(s): 0 
Gene Names: SF3B2SAP145
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentZ [auth 5C]854Homo sapiensMutation(s): 0 
Gene Names: EFTUD2KIAA0031SNRP116
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX23AA [auth 5X]820Homo sapiensMutation(s): 0 
Gene Names: DDX23
EC: 3.6.4.13
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'DA [auth 1b], MA [auth 2b], JB [auth 4b], SA [auth 5b]240Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5EA [auth B5]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AFA [auth 1A]282Homo sapiensMutation(s): 0 
Gene Names: SNRPA
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 1GA [auth S]800Homo sapiensMutation(s): 0 
Gene Names: SART1
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 6IA [auth 5J]850Homo sapiensMutation(s): 0 
Gene Names: PRPF6C20orf14
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IMPC:  MGI:1922946
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
NHP2-like protein 1KA [auth 4D]128Homo sapiensMutation(s): 0 
Gene Names: SNU13NHP2L1
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm3LA [auth 63]102Homo sapiensMutation(s): 0 
Gene Names: LSM3MDS017
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3PA [auth B3]1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GQA [auth 1g], ZA [auth 2g], MB [auth 4g], HB [auth 5g]76Homo sapiensMutation(s): 0 
Gene Names: SNRPGPBSCG
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm8TA [auth 68]96Homo sapiensMutation(s): 0 
Gene Names: LSM8
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8WA [auth 5A]2311Homo sapiensMutation(s): 0 
Gene Names: PRPF8PRPC8
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 3XA [auth A3]501Homo sapiensMutation(s): 0 
Gene Names: SF3A3SAP61
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6.U5 tri-snRNP-associated protein 2YA [auth U]555Homo sapiensMutation(s): 0 
Gene Names: USP39CGI-21HSPC332PRO2855
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Thioredoxin-like protein 4AAB [auth 5D]142Homo sapiensMutation(s): 0 
Gene Names: TXNL4ADIM1TXNL4
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm4DB [auth 64]139Homo sapiensMutation(s): 0 
Gene Names: LSM4
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AFB [auth BP]104Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein CGB [auth 1C]159Homo sapiensMutation(s): 0 
Gene Names: SNRPC
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PRP4 homologIB [auth K]1007Homo sapiensMutation(s): 0 
Gene Names: PRPF4BKIAA0536PRP4PRP4HPRP4K
EC: 2.7.11.1
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
U4/U6 small nuclear ribonucleoprotein Prp3KB [auth 4A]683Homo sapiensMutation(s): 0 
Gene Names: PRPF3HPRP3PRP3
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'OB [auth 2A]255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 1,Splicing factor 3A subunit 1,Splicing factor 3A subunit 1PB [auth A1]647Homo sapiensMutation(s): 0 
Gene Names: SF3A1
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
U6 snRNA-associated Sm-like protein LSm5QB [auth 65]91Homo sapiensMutation(s): 0 
Gene Names: LSM5
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseRB [auth 5B]2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200ASCC3L1HELIC2KIAA0788
EC: 3.6.4.13
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1SB [auth B1]1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U1 snRNAA [auth 1]164Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
U6 snRNAB [auth 6]106Homo sapiens
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Entity ID: 8
MoleculeChainsLengthOrganismImage
AdML pre-mRNAH [auth I]62Human adenovirus 2
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Entity ID: 17
MoleculeChainsLengthOrganismImage
U5 snRNAR [auth 5]117Homo sapiens
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Entity ID: 32
MoleculeChainsLengthOrganismImage
U2 snRNANA [auth 2]188Homo sapiens
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Entity ID: 45
MoleculeChainsLengthOrganismImage
U4 snRNANB [auth 4]146Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomAdG-693087-SPLICE3D
Medical Research Council (United Kingdom)United KingdomMC_U105184330

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references
  • Version 2.0: 2020-10-07
    Changes: Derived calculations, Polymer sequence, Structure summary